Hi Aguera, Regarding dealing with tiling arrays (sorry for top posting): In addition to Marks' suggestions, you might want to have a look at the new AffyTiling package in Bioconductor 2.4, to see what they're doing (I haven't), as well as the older tilingArray and davidTiling packges : * http://www.bioconductor.org/packages/release/bioc/html/AffyTiling.html * http://www.bioconductor.org/packages/release/bioc/html/tilingArray.h tml * http://www.bioconductor.org/packages/release/data/experiment/html/da vidTiling.html Lastly, look at MAT (and the new R-native Bioc 2.4 rMAT packages). They perform analysis over tiling arrays using the *.bpmap files only (I believe): * http://liulab.dfci.harvard.edu/MAT/ * http://www.bioconductor.org/packages/release/bioc/html/rMAT.html HTH, -steve On Apr 24, 2009, at 5:17 AM, Mark Robinson wrote: > Hi Aguera. > > I'm not sure an AffyBatch object is the desired route for Affy > tiling arrays. > > One suggestion would be the combination of 'pdInfoBuilder' to build > a package and oligo::read.celfiles() to read in your data. See > vignettes at: > > http://www.bioconductor.org/packages/release/bioc/html/pdInfoBuilder .html > > If you really really want a CDF file, you might check out: > > http://groups.google.com/group/aroma-affymetrix/web/creating-cdf- files-from-bpmap-files-tiling-arrays > > ... but there are a few judgement calls (e.g. splitting into > "probesets" and so on) that I made there that may not be correct for > what you need. > > Hope that helps. > Mark > > > On 24/04/2009, at 6:35 PM, Elsa Aguera wrote: > >> Hi every body, >> We have to analyse data from Affymetrix microarrays with >> bioconductor and it's the first time we use bioconductor. We work >> with drosophila melanogaster, the chip Type is Dm_tiling2_MR_v01. >> We have a lot of .bpmap file (download in the site of Affymetrix) >> but no cdf file. We can't work without cdf file, and we don't know >> how to get a cdf file. When we try the function ReadAffy this >> message appear : >> >> > ReadAffy("gfpc4.CEL") >> AffyBatch object >> size of arrays=2560x2560 features (7 kb) >> cdf=Dm_tiling2_MR_v01 (??? affyids) >> number of samples=1 >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain Dm_tiling2_MR_v01 >> Library - package dmtiling2mrv01cdf not installed >> Data for package affy did not contain dmtiling2mrv01cdf >> Bioconductor - dmtiling2mrv01cdf not available >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >> >> Actually my question is how we can do to get the cdf file call >> dmtiling2mrv01.cdf ? >> Or can we make a .cdf file with a .bpmap file ? >> >> Someone can explain and help us ? >> thanks >> Aguera >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson at garvan.org.au > e: mrobinson at wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos